@jbrowse/core 5.0.0-beta.4 → 5.0.0-beta.7

package/esm/PluginManager.js

@@ -619,7 +619,7 @@ export default class PluginManager {
             const displays = this.getElementTypesInGroup('display');
             for (const display of displays) {
                 // track may have already added the displayType in its cb
-                if (display.trackType === track.name &&
+                if ([display.trackType].flat().includes(track.name) &&
                     !track.displayTypes.includes(display)) {
                     track.addDisplayType(display);
                 }

package/esm/ReExports/publicUi.d.ts

@@ -1,4 +1,4 @@
 import type { ComponentProps } from 'react';
 declare const LazyBaseTooltip: import("react").LazyExoticComponent<typeof import("../ui/BaseTooltip.tsx").default>;
 export declare function BaseTooltip(props: ComponentProps<typeof LazyBaseTooltip>): import("react").JSX.Element;
-export { ActionLink, AssemblySelector, BaseExportSvgDialog, CONTEXT_MENU_Z_INDEX, CascadingMenu, CascadingMenuButton, ConfirmDialog, ContextMenu, CopyToClipboardButton, Crosshairs, Dialog, EditableTypography, ErrorBanner, ErrorBar, ErrorMessage, ErrorOverlay, ExportSvgDialog, ExternalLink, FatalErrorDialog, FileDropZone, FileSelector, GRADIENT_LEGEND_HEIGHT, GRADIENT_LEGEND_SVG_AREA_WIDTH, GRADIENT_LEGEND_WIDTH, GpuFallbackButton, INLINE_MENU_ROW_WIDTH, InfoDialog, JexlFilterDialog, LAUNCH_LABEL, LEGEND_ROW_HEIGHT, LEGEND_SWATCH, LabeledCheckbox, LegendSwatchGlyph, LoadingEllipses, LoadingOverlay, LoadingProgress, LogoFull, Logomark, MAX_LEGEND_ITEMS, Menu, MonospaceTextField, NumberTextField, PinAdornment, PluggableComponent, PluggableComponents, PluggableElements, PrerenderedCanvas, ProgressChip, RefNameAutocomplete, RefNameAutocompleteEndAdornment, ReplaceCurrentViewButton, ResetToDefaultButton, ResizeHandle, SanitizedHTML, ScrollChrome, ScrollEdgeShadow, SettingsChangesTable, ShareLinkField, SingleSlider, SliderTooltip, StatusProgressBar, SubmitDialog, SubmitForm, SvgColorLegend, SvgGradientLegend, TOOLTIP_Z_INDEX, TagTextField, VIEW_HEADER_HEIGHT, VerticalScrollbar, ViewLoadingScreen, addExtensionElement, adornmentReservePx, checkboxItem, colorFwdStrand, colorInterchrom, colorLongInsert, colorLongreadInv, colorNeutralRead, colorPairLL, colorPairLR, colorPairLRDark, colorPairRL, colorPairRR, colorRevStrand, colorShortInsert, colorSplitReadInversion, colorSupplementary, colorUnmappedMate, colorUnmappedMateDark, createJBrowseBaseTheme, createJBrowseTheme, createJBrowseThemeFromArgs, defaultThemes, displayTypesWithPromotableSlots, getInputWidth, hoverBoxStyle, launchTargetsMenuItem, legendEntries, legendIsReadable, legendSwatches, makePromotableSizeMenu, makeSizeMenu, makeSizeSubMenu, matchesTrackSelector, measureLegendText, methylated5hmC, methylated5mC, misKindedPins, nonEmptyLegendSections, promotableSlotsWithoutPin, pushIntoSubMenu, pushLaunchViewMenuItem, radioItems, replaceViewAction, resolveSubMenu, sliderScale, staysOpenOnClick, tagColorPalette, unmethylated5mC, useAssemblySelection, useCopyToClipboard, useExportSvgPreference, useMouseState, useMouseTracking, useRecentLocations, wrapComponent, } from '../ui/index.ts';
+export { ActionLink, AssemblySelector, BaseExportSvgDialog, CONTEXT_MENU_Z_INDEX, CascadingMenu, CascadingMenuButton, ConfirmDialog, ContextMenu, CopyToClipboardButton, Crosshairs, Dialog, EditableTypography, ErrorBanner, ErrorBar, ErrorMessage, ErrorOverlay, ExportSvgDialog, ExternalLink, FatalErrorDialog, FileDropZone, FileSelector, GpuFallbackButton, INLINE_MENU_ROW_WIDTH, InfoDialog, JexlFilterDialog, LAUNCH_LABEL, LEGEND_ROW_HEIGHT, LEGEND_SVG_GUTTER_WIDTH, LEGEND_SWATCH, LabeledCheckbox, LegendSwatchGlyph, LoadingEllipses, LoadingOverlay, LoadingProgress, LogoFull, Logomark, MAX_LEGEND_ITEMS, Menu, MonospaceTextField, NumberTextField, PluggableComponent, PluggableComponents, PluggableElements, PrerenderedCanvas, ProgressChip, RefNameAutocomplete, RefNameAutocompleteEndAdornment, ReplaceCurrentViewButton, ResetToDefaultButton, ResizeHandle, SanitizedHTML, ScrollChrome, ScrollEdgeShadow, SettingsChangesTable, ShareLinkField, SingleSlider, SliderTooltip, StatusProgressBar, SubmitDialog, SubmitForm, SvgColorLegend, TOOLTIP_Z_INDEX, TagTextField, VIEW_HEADER_HEIGHT, VerticalScrollbar, ViewLoadingScreen, addExtensionElement, adornmentReservePx, checkboxItem, colorFwdStrand, colorInterchrom, colorLongInsert, colorLongreadInv, colorNeutralRead, colorPairLL, colorPairLR, colorPairLRDark, colorPairRL, colorPairRR, colorRevStrand, colorScaleIsEmpty, colorShortInsert, colorSplitReadInversion, colorSupplementary, colorUnmappedMate, colorUnmappedMateDark, createJBrowseBaseTheme, createJBrowseTheme, createJBrowseThemeFromArgs, defaultThemes, getInputWidth, hoverBoxStyle, launchTargetsMenuItem, legendEntries, legendIsReadable, legendSpecOf, legendSwatches, makeSizeMenu, makeSizeSubMenu, matchesTrackSelector, measureLegendText, methylated5hmC, methylated5mC, nonEmptyLegendSections, pushIntoSubMenu, pushLaunchViewMenuItem, radioItems, replaceViewAction, resolveSubMenu, sliderScale, staysOpenOnClick, tagColorPalette, unmethylated5mC, useAssemblySelection, useCopyToClipboard, useExportSvgPreference, useMouseState, useMouseTracking, useRecentLocations, wrapComponent, } from '../ui/index.ts';

package/esm/ReExports/publicUi.js

@@ -30,4 +30,4 @@ const LazyBaseTooltip = lazy(() => import('../ui/BaseTooltip.js'));
 export function BaseTooltip(props) {
     return (_jsx(Suspense, { fallback: null, children: _jsx(LazyBaseTooltip, { ...props }) }));
 }
-export { ActionLink, AssemblySelector, BaseExportSvgDialog, CONTEXT_MENU_Z_INDEX, CascadingMenu, CascadingMenuButton, ConfirmDialog, ContextMenu, CopyToClipboardButton, Crosshairs, Dialog, EditableTypography, ErrorBanner, ErrorBar, ErrorMessage, ErrorOverlay, ExportSvgDialog, ExternalLink, FatalErrorDialog, FileDropZone, FileSelector, GRADIENT_LEGEND_HEIGHT, GRADIENT_LEGEND_SVG_AREA_WIDTH, GRADIENT_LEGEND_WIDTH, GpuFallbackButton, INLINE_MENU_ROW_WIDTH, InfoDialog, JexlFilterDialog, LAUNCH_LABEL, LEGEND_ROW_HEIGHT, LEGEND_SWATCH, LabeledCheckbox, LegendSwatchGlyph, LoadingEllipses, LoadingOverlay, LoadingProgress, LogoFull, Logomark, MAX_LEGEND_ITEMS, Menu, MonospaceTextField, NumberTextField, PinAdornment, PluggableComponent, PluggableComponents, PluggableElements, PrerenderedCanvas, ProgressChip, RefNameAutocomplete, RefNameAutocompleteEndAdornment, ReplaceCurrentViewButton, ResetToDefaultButton, ResizeHandle, SanitizedHTML, ScrollChrome, ScrollEdgeShadow, SettingsChangesTable, ShareLinkField, SingleSlider, SliderTooltip, StatusProgressBar, SubmitDialog, SubmitForm, SvgColorLegend, SvgGradientLegend, TOOLTIP_Z_INDEX, TagTextField, VIEW_HEADER_HEIGHT, VerticalScrollbar, ViewLoadingScreen, addExtensionElement, adornmentReservePx, checkboxItem, colorFwdStrand, colorInterchrom, colorLongInsert, colorLongreadInv, colorNeutralRead, colorPairLL, colorPairLR, colorPairLRDark, colorPairRL, colorPairRR, colorRevStrand, colorShortInsert, colorSplitReadInversion, colorSupplementary, colorUnmappedMate, colorUnmappedMateDark, createJBrowseBaseTheme, createJBrowseTheme, createJBrowseThemeFromArgs, defaultThemes, displayTypesWithPromotableSlots, getInputWidth, hoverBoxStyle, launchTargetsMenuItem, legendEntries, legendIsReadable, legendSwatches, makePromotableSizeMenu, makeSizeMenu, makeSizeSubMenu, matchesTrackSelector, measureLegendText, methylated5hmC, methylated5mC, misKindedPins, nonEmptyLegendSections, promotableSlotsWithoutPin, pushIntoSubMenu, pushLaunchViewMenuItem, radioItems, replaceViewAction, resolveSubMenu, sliderScale, staysOpenOnClick, tagColorPalette, unmethylated5mC, useAssemblySelection, useCopyToClipboard, useExportSvgPreference, useMouseState, useMouseTracking, useRecentLocations, wrapComponent, } from '../ui/index.js';
+export { ActionLink, AssemblySelector, BaseExportSvgDialog, CONTEXT_MENU_Z_INDEX, CascadingMenu, CascadingMenuButton, ConfirmDialog, ContextMenu, CopyToClipboardButton, Crosshairs, Dialog, EditableTypography, ErrorBanner, ErrorBar, ErrorMessage, ErrorOverlay, ExportSvgDialog, ExternalLink, FatalErrorDialog, FileDropZone, FileSelector, GpuFallbackButton, INLINE_MENU_ROW_WIDTH, InfoDialog, JexlFilterDialog, LAUNCH_LABEL, LEGEND_ROW_HEIGHT, LEGEND_SVG_GUTTER_WIDTH, LEGEND_SWATCH, LabeledCheckbox, LegendSwatchGlyph, LoadingEllipses, LoadingOverlay, LoadingProgress, LogoFull, Logomark, MAX_LEGEND_ITEMS, Menu, MonospaceTextField, NumberTextField, PluggableComponent, PluggableComponents, PluggableElements, PrerenderedCanvas, ProgressChip, RefNameAutocomplete, RefNameAutocompleteEndAdornment, ReplaceCurrentViewButton, ResetToDefaultButton, ResizeHandle, SanitizedHTML, ScrollChrome, ScrollEdgeShadow, SettingsChangesTable, ShareLinkField, SingleSlider, SliderTooltip, StatusProgressBar, SubmitDialog, SubmitForm, SvgColorLegend, TOOLTIP_Z_INDEX, TagTextField, VIEW_HEADER_HEIGHT, VerticalScrollbar, ViewLoadingScreen, addExtensionElement, adornmentReservePx, checkboxItem, colorFwdStrand, colorInterchrom, colorLongInsert, colorLongreadInv, colorNeutralRead, colorPairLL, colorPairLR, colorPairLRDark, colorPairRL, colorPairRR, colorRevStrand, colorScaleIsEmpty, colorShortInsert, colorSplitReadInversion, colorSupplementary, colorUnmappedMate, colorUnmappedMateDark, createJBrowseBaseTheme, createJBrowseTheme, createJBrowseThemeFromArgs, defaultThemes, getInputWidth, hoverBoxStyle, launchTargetsMenuItem, legendEntries, legendIsReadable, legendSpecOf, legendSwatches, makeSizeMenu, makeSizeSubMenu, matchesTrackSelector, measureLegendText, methylated5hmC, methylated5mC, nonEmptyLegendSections, pushIntoSubMenu, pushLaunchViewMenuItem, radioItems, replaceViewAction, resolveSubMenu, sliderScale, staysOpenOnClick, tagColorPalette, unmethylated5mC, useAssemblySelection, useCopyToClipboard, useExportSvgPreference, useMouseState, useMouseTracking, useRecentLocations, wrapComponent, } from '../ui/index.js';

package/esm/ReExports/publicUtil.d.ts

@@ -1 +1 @@
-export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGeneLikeType, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSequenceMatchType, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, scheduleDetachedDestroy, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.ts';
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGeneLikeType, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSequenceMatchType, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, scheduleDetachedDestroy, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.ts';

package/esm/ReExports/publicUtil.js

@@ -29,4 +29,4 @@
 // its barrel does not export, behind lazy(). That is what makes "take it out of
 // the barrel so it leaves the startup path" a different edit from "stop serving
 // it to plugins", which here they were not.
-export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGeneLikeType, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSequenceMatchType, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, scheduleDetachedDestroy, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.js';
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGeneLikeType, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSequenceMatchType, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, scheduleDetachedDestroy, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.js';

package/esm/ReExports/workerNamespaceNames.js

@@ -143,15 +143,13 @@ export const CORE_UI_NAMES = [
     'FatalErrorDialog',
     'FileDropZone',
     'FileSelector',
-    'GRADIENT_LEGEND_HEIGHT',
-    'GRADIENT_LEGEND_SVG_AREA_WIDTH',
-    'GRADIENT_LEGEND_WIDTH',
     'GpuFallbackButton',
     'INLINE_MENU_ROW_WIDTH',
     'InfoDialog',
     'JexlFilterDialog',
     'LAUNCH_LABEL',
     'LEGEND_ROW_HEIGHT',
+    'LEGEND_SVG_GUTTER_WIDTH',
     'LEGEND_SWATCH',
     'LabeledCheckbox',
     'LegendSwatchGlyph',
@@ -164,7 +162,6 @@ export const CORE_UI_NAMES = [
     'Menu',
     'MonospaceTextField',
     'NumberTextField',
-    'PinAdornment',
     'PluggableComponent',
     'PluggableComponents',
     'PluggableElements',
@@ -186,7 +183,6 @@ export const CORE_UI_NAMES = [
     'SubmitDialog',
     'SubmitForm',
     'SvgColorLegend',
-    'SvgGradientLegend',
     'TOOLTIP_Z_INDEX',
     'TagTextField',
     'VIEW_HEADER_HEIGHT',
@@ -206,6 +202,7 @@ export const CORE_UI_NAMES = [
     'colorPairRL',
     'colorPairRR',
     'colorRevStrand',
+    'colorScaleIsEmpty',
     'colorShortInsert',
     'colorSplitReadInversion',
     'colorSupplementary',
@@ -215,23 +212,20 @@ export const CORE_UI_NAMES = [
     'createJBrowseTheme',
     'createJBrowseThemeFromArgs',
     'defaultThemes',
-    'displayTypesWithPromotableSlots',
     'getInputWidth',
     'hoverBoxStyle',
     'launchTargetsMenuItem',
     'legendEntries',
     'legendIsReadable',
+    'legendSpecOf',
     'legendSwatches',
-    'makePromotableSizeMenu',
     'makeSizeMenu',
     'makeSizeSubMenu',
     'matchesTrackSelector',
     'measureLegendText',
     'methylated5hmC',
     'methylated5mC',
-    'misKindedPins',
     'nonEmptyLegendSections',
-    'promotableSlotsWithoutPin',
     'pushIntoSubMenu',
     'pushLaunchViewMenuItem',
     'radioItems',

package/esm/assemblyManager/assemblyConfigSchema.d.ts

@@ -84,7 +84,8 @@ export { expandAssemblySequenceAdapter, expandAssemblyShorthand, } from './expan
  * #example custom-display-name-and-genetic-codes-sidecar
  * Sets a `displayName` for the assembly selector and loads the per-refName
  * genetic codes from a sidecar TSV (`geneticCodesLocation`) instead of inlining
- * them — handy when a config generator emits the mapping separately:
+ * them, which is the shape to use when a config generator emits the mapping
+ * separately:
  * ```js
  * {
  *   name: 'hg38',

package/esm/assemblyManager/assemblyConfigSchema.js

@@ -84,7 +84,8 @@ export { expandAssemblySequenceAdapter, expandAssemblyShorthand, } from './expan
  * #example custom-display-name-and-genetic-codes-sidecar
  * Sets a `displayName` for the assembly selector and loads the per-refName
  * genetic codes from a sidecar TSV (`geneticCodesLocation`) instead of inlining
- * them — handy when a config generator emits the mapping separately:
+ * them, which is the shape to use when a config generator emits the mapping
+ * separately:
  * ```js
  * {
  *   name: 'hg38',

package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts

@@ -1,19 +1,4 @@
 import type PluginManager from '../PluginManager.ts';
-/**
- * Fill in an assembly `sequence.adapter`'s `type` from its `uri` when the type
- * is omitted, so `sequence: { adapter: { uri: 'genome.fa.gz' } }` resolves to a
- * `BgzipFastaAdapter` (and `.fa` → indexed, `.2bit` → `TwoBitAdapter`). Uses the
- * same `Core-guessAdapterForLocation` extension point the "Add track" flow uses,
- * so every host describes a custom genome with just a URL and lets jbrowse-core
- * pick the adapter — no adapter-type table in the Python/R/JS bindings.
- *
- * The guesser also derives the index locations (`.fai`/`.gzi`) from the uri;
- * explicit adapter fields (e.g. a non-sibling `faiLocation`) are spread on top
- * so they win. A `uri` matching no sequence adapter is left untouched, so a
- * genuinely bad config still surfaces its own downstream error. Returns the same
- * object reference when there is nothing to expand, so callers can cheaply skip
- * a rebuild.
- */
 /**
  * Expand an assembly snapshot's own shorthands into the `sequence` an assembly
  * config declares: the flat `{ name, uri: 'genome.fa.gz' }` form, the
@@ -29,4 +14,19 @@ import type PluginManager from '../PluginManager.ts';
  * consumed, so the schema's own later pass finds nothing to do.
  */
 export declare function expandAssemblyShorthand<T>(snap: T, pluginManager: PluginManager): T;
+/**
+ * Fill in an assembly `sequence.adapter`'s `type` from its `uri` when the type
+ * is omitted, so `sequence: { adapter: { uri: 'genome.fa.gz' } }` resolves to a
+ * `BgzipFastaAdapter` (and `.fa` → indexed, `.2bit` → `TwoBitAdapter`). Uses the
+ * same `Core-guessAdapterForLocation` extension point the "Add track" flow uses,
+ * so every host describes a custom genome with just a URL and lets jbrowse-core
+ * pick the adapter — no adapter-type table in the Python/R/JS bindings.
+ *
+ * Only the type comes off the guess: the adapter's own `normalizeSnapshot`
+ * expands the `uri` into the location slots it declares, so the shorthand
+ * expands to the same thing here as it does when the config names the type.
+ * A `uri` matching no sequence adapter is left untouched, and the same object
+ * reference comes back when there is nothing to expand, so callers can cheaply
+ * skip a rebuild.
+ */
 export declare function expandAssemblySequenceAdapter(sequence: unknown, pluginManager: PluginManager): unknown;

package/esm/assemblyManager/expandAssemblyConfigShorthand.js

@@ -2,21 +2,6 @@ import { UNKNOWN } from '../util/tracks.js';
 function isPlainObject(v) {
     return typeof v === 'object' && v !== null && !Array.isArray(v);
 }
-/**
- * Fill in an assembly `sequence.adapter`'s `type` from its `uri` when the type
- * is omitted, so `sequence: { adapter: { uri: 'genome.fa.gz' } }` resolves to a
- * `BgzipFastaAdapter` (and `.fa` → indexed, `.2bit` → `TwoBitAdapter`). Uses the
- * same `Core-guessAdapterForLocation` extension point the "Add track" flow uses,
- * so every host describes a custom genome with just a URL and lets jbrowse-core
- * pick the adapter — no adapter-type table in the Python/R/JS bindings.
- *
- * The guesser also derives the index locations (`.fai`/`.gzi`) from the uri;
- * explicit adapter fields (e.g. a non-sibling `faiLocation`) are spread on top
- * so they win. A `uri` matching no sequence adapter is left untouched, so a
- * genuinely bad config still surfaces its own downstream error. Returns the same
- * object reference when there is nothing to expand, so callers can cheaply skip
- * a rebuild.
- */
 /**
  * Expand an assembly snapshot's own shorthands into the `sequence` an assembly
  * config declares: the flat `{ name, uri: 'genome.fa.gz' }` form, the
@@ -60,6 +45,21 @@ export function expandAssemblyShorthand(snap, pluginManager) {
     // preserve the identity-unchanged case so nothing rebuilds needlessly
     return (sequence === snap.sequence ? snap : { ...rest, name, sequence });
 }
+/**
+ * Fill in an assembly `sequence.adapter`'s `type` from its `uri` when the type
+ * is omitted, so `sequence: { adapter: { uri: 'genome.fa.gz' } }` resolves to a
+ * `BgzipFastaAdapter` (and `.fa` → indexed, `.2bit` → `TwoBitAdapter`). Uses the
+ * same `Core-guessAdapterForLocation` extension point the "Add track" flow uses,
+ * so every host describes a custom genome with just a URL and lets jbrowse-core
+ * pick the adapter — no adapter-type table in the Python/R/JS bindings.
+ *
+ * Only the type comes off the guess: the adapter's own `normalizeSnapshot`
+ * expands the `uri` into the location slots it declares, so the shorthand
+ * expands to the same thing here as it does when the config names the type.
+ * A `uri` matching no sequence adapter is left untouched, and the same object
+ * reference comes back when there is nothing to expand, so callers can cheaply
+ * skip a rebuild.
+ */
 export function expandAssemblySequenceAdapter(sequence, pluginManager) {
     const adapter = isPlainObject(sequence) ? sequence.adapter : undefined;
     if (isPlainObject(sequence) &&
@@ -77,9 +77,25 @@ export function expandAssemblySequenceAdapter(sequence, pluginManager) {
             ...(typeof baseUri === 'string' ? { baseUri } : {}),
         };
         const guess = guesser(file, undefined);
-        return guess && guess.type !== UNKNOWN
-            ? { ...sequence, adapter: { ...guess, ...extras } }
-            : sequence;
+        if (!guess || guess.type === UNKNOWN) {
+            return sequence;
+        }
+        // the type is the only thing the guess is needed for. The adapter's own
+        // normalizeSnapshot expands `uri` and everything riding with it — a 2bit's
+        // `chromSizes`, which the guess has no slot for and MST then dropped
+        // unannounced — so this is not a second place that knows how a sequence
+        // file names its sidecars. An adapter declaring no shorthand keeps the
+        // guess's derived locations.
+        const normalize = pluginManager.hasAdapterType(guess.type)
+            ? pluginManager.getAdapterType(guess.type).normalizeSnapshot
+            : undefined;
+        const shorthand = { ...adapter, type: guess.type };
+        const normalized = normalize?.(shorthand) ?? shorthand;
+        // `uri` is consumed, and it has to GO: localFiles substitutes a blob into a
+        // location node, and an adapter still carrying `uri` reads as one
+        const full = normalized === shorthand ? { ...guess, ...extras } : normalized;
+        const { uri: _consumed, baseUri: _spent, ...expanded } = full;
+        return { ...sequence, adapter: expanded };
     }
     return sequence;
 }

package/esm/configuration/configurationSchema.d.ts

@@ -70,8 +70,7 @@ export declare function ConfigurationSchema<const DEFINITION extends Configurati
  * objects until something references a track (ADR-031), so a caller handed one
  * of those has a config that reads nothing but what was literally authored: a
  * slot at its schema default is absent, `preProcessSnapshot` has not run, and
- * nothing that walks a live node — the promotable cascade above all — applies
- * to it.
+ * nothing that walks a live node applies to it.
  *
  * For the callers that need the resolved answer rather than the authored one
  * and cannot know which of the two they were handed. The About dialog's "Copy

package/esm/configuration/configurationSchema.js

@@ -20,12 +20,8 @@ function chainHooks(base, child) {
  * **redeclares merges field-by-field over the base's** — so an override states
  * only what actually differs and inherits the rest. (`type` comes along
  * regardless: it is what marks an entry as a slot rather than a nested
- * sub-schema, per `isSlotDefinitionEntry`.)
- *
- * A subclass that really wants a plain slot states `promotedBase: undefined`,
- * which works *because* this is a spread: a stated `undefined` overwrites the
- * base's value where an omitted key would inherit it. The four cases are pinned
- * by the "baseConfiguration slot override merge" tests.
+ * sub-schema, per `isSlotDefinitionEntry`.) The cases are pinned by the
+ * "baseConfiguration slot override merge" tests.
  */
 function mergeSchemaDefinition(baseDefinition, childDefinition) {
     const merged = {
@@ -266,8 +262,7 @@ function hydrateInto(pluginManager, schemaType, frozen) {
  * objects until something references a track (ADR-031), so a caller handed one
  * of those has a config that reads nothing but what was literally authored: a
  * slot at its schema default is absent, `preProcessSnapshot` has not run, and
- * nothing that walks a live node — the promotable cascade above all — applies
- * to it.
+ * nothing that walks a live node applies to it.
  *
  * For the callers that need the resolved answer rather than the authored one
  * and cannot know which of the two they were handed. The About dialog's "Copy

package/esm/configuration/configurationSlot.d.ts

@@ -179,53 +179,6 @@ interface ConfigSlotDefinitionCommon {
      * editor, so common slots aren't crowded out by rarely-changed ones
      */
     advanced?: boolean;
-    /**
-     * **Declaring this makes the slot promotable**, and it is the only thing that
-     * does: a user can promote the slot's value to a session-wide default for all
-     * tracks of the same display type (the track-menu pin). An *unset* slot
-     * follows (inherits) that promoted default; any concrete value customizes the
-     * track. Read it with `resolveConf`, never `getConf`; see
-     * `promotableResolve.ts`.
-     *
-     * The value itself is what the unset state resolves to when a track inherits
-     * and nothing is promoted. This is the CSS model — being unset is the
-     * `inherit` keyword and `promotedBase` is `initial` (the value at the bottom
-     * of the cascade). Spending only `undefined` on the sentinel is what leaves
-     * every *real* value — `promotedBase` included — customizable over an opposite
-     * session default, so a track can hold `displayMode: 'normal'` under a
-     * promoted `'compact'`.
-     *
-     * Requires a `maybe*` slot type (whose `undefined` is the inherit sentinel)
-     * and no `defaultValue`; `ConfigSlot` throws otherwise, and both stay runtime
-     * checks. Forbidding it on the plain half of `ConfigSlotDefinition` was tried:
-     * it forces a cast into `mergeSchemaDefinition`, whose spread of two slot
-     * definitions lands in neither member, and buys only an earlier version of a
-     * throw that already fires when the schema is built.
-     *
-     * A subclass turns an inherited promotable slot back into a plain one by
-     * stating `promotedBase: undefined` — the definition merge is a spread, so a
-     * stated `undefined` really does overwrite the base's value.
-     */
-    promotedBase?: unknown;
-    /**
-     * For a promotable slot: an extra semantic check a stored value must pass,
-     * on top of the built-in type-shape check, before the cascade
-     * (`promotableResolve.ts`'s `isUsableValue`) treats it as usable. Applies to
-     * both cascade tiers — a session-wide promoted default and a track's own saved
-     * value. Needed when a slot's shape alone can't catch a semantically-invalid
-     * value — e.g. alignments `colorBy`'s `.type` must name a currently-registered
-     * color scheme, not just be *some* string — so a stale scheme name (renamed or
-     * removed since the value was saved) degrades to "not usable" (falls back to
-     * the base) instead of reaching a lookup that assumes every `.type` is
-     * registered. Omit when the type-shape check alone is enough to trust the value.
-     *
-     * Runs at **schema build** too, over the slot's own `promotedBase` — the base
-     * is what every failing tier degrades to, so it has to clear the same bar.
-     * Keep the hook a function of module-level data (as `isRegisteredColorScheme`
-     * is of `COLOR_SCHEMES`); one that consults state its plugin registers later
-     * during `install()` would reject a base that is really fine.
-     */
-    validate?: (value: unknown) => boolean;
 }
 /**
  * A slot definition, split on whether the slot's type spends `undefined` on

package/esm/configuration/configurationSlot.js

@@ -1,8 +1,6 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { freezeDeep } from '../util/freezeDeep.js';
 import { isJexl, stringToJexlExpression } from '../util/jexlStrings.js';
 import { FileLocation } from '../util/types/mst.js';
-import { isUsableValue } from './slotShape.js';
 import { isCallbackValue } from './slotValueUtils.js';
 // Single source of truth for the builtin slot type names, pairing each with its
 // MST value type and its editor fallback default. Keeping model + fallback in
@@ -28,9 +26,7 @@ const slotTypes = {
     number: { model: types.number, fallbackDefault: 1 },
     // The `maybe*` types spend `undefined` on "not explicitly set", which is the
     // one value no config can spell and so the only reliable way to say it — a
-    // computed/auto fallback (a drag-resized track height), or the inherit
-    // sentinel every promotable slot needs (pair with `promotedBase`, and read
-    // with `resolveConf`).
+    // computed/auto fallback, e.g. a drag-resized track height.
     maybeNumber: { model: types.maybe(types.number) },
     maybeBoolean: { model: types.maybe(types.boolean) },
     // for a slot whose unset state means "decide from the data" — a feature's own
@@ -97,7 +93,7 @@ const JexlStringType = types.refinement('JexlString', types.string, isJexl);
  * evaluated on read by `readConfObject`.
  */
 export default function ConfigSlot(definition) {
-    const { model, type, defaultValue, promotedBase } = definition;
+    const { model, type, defaultValue } = definition;
     if (!CONFIG_SLOT_TYPE_NAMES.has(type)) {
         throw new Error(`config slot needs a known type name, got ${JSON.stringify(type)}`);
     }
@@ -111,49 +107,6 @@ export default function ConfigSlot(definition) {
     if (defaultValue === undefined && !MAYBE_TYPES.has(type)) {
         throw new Error("no 'defaultValue' provided");
     }
-    // `promotedBase` is what makes a slot promotable, so its presence is the whole
-    // condition here (ADR-047).
-    //
-    // A promotable slot spends being-unset on the inherit sentinel, so it must be a
-    // `maybe*` type. Any *concrete* default would double as the inherit signal,
-    // making that one value un-customizable under an opposite promoted default — an
-    // authoring mistake with no runtime symptom other than a setting that won't
-    // stay put, so fail at construction.
-    if (promotedBase !== undefined) {
-        if (!MAYBE_TYPES.has(type)) {
-            throw new Error(`a 'promotedBase' slot needs a maybe* type whose undefined is the inherit sentinel, not "${type}"`);
-        }
-        if (defaultValue !== undefined) {
-            throw new Error("a promotable slot must leave 'defaultValue' undefined — that IS the inherit sentinel; 'promotedBase' is what an unset slot resolves to");
-        }
-        // The base is the bottom of the cascade: every other tier that fails
-        // `isUsableValue` falls back to it, so a base that would itself fail has
-        // nowhere left to fall and every read of the slot returns a value no
-        // consumer handles — with nothing thrown anywhere. The typo this catches is
-        // a `promotedBase` outside the slot's own vocabulary (an enum member not in
-        // `model`, a non-finite number), which nothing else in the system checks.
-        if (!isUsableValue(definition, promotedBase)) {
-            throw new Error(`a 'promotedBase' must be a value the slot can hold: ${JSON.stringify(promotedBase)} is not a valid "${type}"`);
-        }
-        // A promotable slot cannot hold a callback: `isUsableValue` refuses a
-        // `jexl:` value at both cascade tiers, so one written into the slot is
-        // discarded straight back to the base. `contextVariable` is the only thing
-        // that offers writing one — it is what raises the config editor's jexl
-        // toggle (`SlotEditor`) — so the pair is a control whose every write the
-        // cascade throws away, with nothing thrown anywhere. Nothing else in the
-        // system states this; DISPLAY_TYPE_DEFAULTS.md §"No callbacks" only
-        // describes the read side.
-        if (definition.contextVariable?.length) {
-            throw new Error("a promotable slot ('promotedBase') cannot declare 'contextVariable': the cascade refuses a jexl: callback, so the config editor would offer a toggle whose writes silently degrade back to the base");
-        }
-        // The resolver hands `promotedBase` out by reference, so an object-valued one
-        // (`maybeFrozen`, e.g. alignments `colorBy`) is one literal shared live by
-        // every track sitting at base. Freeze it here, the only place it enters the
-        // system, so mutating a resolved value throws instead of silently rewriting
-        // the default for every other track — and for every later session, since this
-        // object belongs to the schema. See `freezeDeep` for why by-reference stays.
-        freezeDeep(promotedBase);
-    }
     // The inverse of the `defaultValue === undefined` check above, and the half
     // that had no guard. A `maybe*` slot whose default is concrete can never *be*
     // unset — no config can spell `undefined` — so the unset state such a slot
@@ -161,8 +114,6 @@ export default function ConfigSlot(definition) {
     // and the branch reading it never runs. There is no symptom: the slot reads as
     // a perfectly good value everywhere.
     //
-    // Last, so a promotable slot still gets the more specific message above.
-    //
     // The way this happens is **inheritance**, which is why the type can't catch
     // it: a `maybe*` override of a plain base slot inherits the base's concrete
     // default through the definition spread, and the override's own literal looks
@@ -173,9 +124,8 @@ export default function ConfigSlot(definition) {
     }
     return types.stripDefault(types.union(JexlStringType, 
     // `maybeStringEnum` is the only maybe type whose model comes from the
-    // author: they write the plain vocabulary (`['fixed','grow','fit']`) and
-    // the nullability is added here, so no enumeration has to carry a fake
-    // member for the cascade's benefit.
+    // author: they write the plain vocabulary and the nullability is added
+    // here.
     type === 'maybeStringEnum' ? types.maybe(valueModel) : valueModel), defaultValue);
 }
 /**

package/esm/configuration/fillLocations.d.ts

@@ -0,0 +1,14 @@
+/**
+ * A shorthand snapshot with its location slots filled in: `derived` supplies
+ * what the shorthand implies, and any key the config spells out for itself
+ * wins.
+ *
+ * Spread the other way round — derived over the snapshot — a config naming both
+ * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
+ * faiLocation: { uri: 'custom.fai' } }`, silently lost the index it named to
+ * the one the shorthand invents. Every adapter's normalizer had its own copy of
+ * the spread, so the precedence had to be got right 30-odd times.
+ */
+export declare function fillLocations(snap: Record<string, unknown>, derived: Record<string, unknown>): {
+    [x: string]: unknown;
+};

package/esm/configuration/fillLocations.js

@@ -0,0 +1,14 @@
+/**
+ * A shorthand snapshot with its location slots filled in: `derived` supplies
+ * what the shorthand implies, and any key the config spells out for itself
+ * wins.
+ *
+ * Spread the other way round — derived over the snapshot — a config naming both
+ * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
+ * faiLocation: { uri: 'custom.fai' } }`, silently lost the index it named to
+ * the one the shorthand invents. Every adapter's normalizer had its own copy of
+ * the spread, so the precedence had to be got right 30-odd times.
+ */
+export function fillLocations(snap, derived) {
+    return { ...derived, ...snap };
+}

package/esm/configuration/fullConfSnapshot.d.ts

@@ -7,21 +7,6 @@ import type { AnyConfigurationModel } from './types.ts';
  * schema. JEXL callback slots keep their raw `"jexl:..."` string for the worker
  * to evaluate per-feature.
  *
- * **Why this isn't exported from `@jbrowse/core/configuration`.** It was
- * (as `getConfSnapshot`), and being reachable was the hazard. A promotable slot
- * resolves against the session at read time, so snapshotting one raw ships the
- * bare `undefined` inherit sentinel to a worker with no session to resolve it
- * against — and every display in the repo now has promotable slots. The public
- * form used to defend itself by *throwing* on such a config, which meant the
- * obvious spelling in a new `rpcProps()` failed at runtime, on the first fetch,
- * in whichever product exercised that display. Off the barrel, the same mistake
- * is an unresolved import: it can't be written at all, and
- * `getConfigSnapshotWithPromotables(display)` is the one way across the boundary.
- * So this is the shared walker those resolvers are built on, not an entry point.
- *
- * The nested-schema guard below is the part of that defense still worth
- * enforcing at runtime, since no import can express it.
- *
  * Note: only handles slots and direct sub-configuration models. Arrays or maps
  * of sub-schemas are silently dropped — nothing has needed them.
  */

package/esm/configuration/fullConfSnapshot.js

@@ -1,5 +1,4 @@
 import { getSnapshot, isArrayType, isMapType, isStateTreeNode, } from '@jbrowse/mobx-state-tree';
-import { promotableSlotNames } from './promotableSlots.js';
 import { getConfigurationSchemaDefinition } from './schemaRegistry.js';
 import { isConfigurationModel, isConfigurationSchemaType, isSlotDefinitionEntry, } from './schemaTypes.js';
 /**
@@ -10,21 +9,6 @@ import { isConfigurationModel, isConfigurationSchemaType, isSlotDefinitionEntry,
  * schema. JEXL callback slots keep their raw `"jexl:..."` string for the worker
  * to evaluate per-feature.
  *
- * **Why this isn't exported from `@jbrowse/core/configuration`.** It was
- * (as `getConfSnapshot`), and being reachable was the hazard. A promotable slot
- * resolves against the session at read time, so snapshotting one raw ships the
- * bare `undefined` inherit sentinel to a worker with no session to resolve it
- * against — and every display in the repo now has promotable slots. The public
- * form used to defend itself by *throwing* on such a config, which meant the
- * obvious spelling in a new `rpcProps()` failed at runtime, on the first fetch,
- * in whichever product exercised that display. Off the barrel, the same mistake
- * is an unresolved import: it can't be written at all, and
- * `getConfigSnapshotWithPromotables(display)` is the one way across the boundary.
- * So this is the shared walker those resolvers are built on, not an entry point.
- *
- * The nested-schema guard below is the part of that defense still worth
- * enforcing at runtime, since no import can express it.
- *
  * Note: only handles slots and direct sub-configuration models. Arrays or maps
  * of sub-schemas are silently dropped — nothing has needed them.
  */
@@ -47,20 +31,8 @@ export function fullConfSnapshot(confObject) {
             // array/map type carries no registered slot table, so recursing would
             // emit a meaningless `{}` (a type-confusion hazard for a consumer
             // expecting the array). Constants are skipped entirely.
-            assertNoPromotableSlots(v);
             result[key] = fullConfSnapshot(v);
         }
     }
     return result;
 }
-// A promotable slot is only ever resolvable at a config's own top level — the
-// resolver walks that one slot table (`promotableSlotNames` / `getSlotDefinition`)
-// and never descends. So one declared inside a *nested* schema would resolve
-// nowhere and serialize as its bare inherit sentinel, with no import to get wrong
-// and no symptom until a worker read the sentinel. Fail at the snapshot instead.
-function assertNoPromotableSlots(confObject) {
-    const promotable = promotableSlotNames(confObject);
-    if (promotable.size > 0) {
-        throw new Error(`nested config schema declares promotable slots (${[...promotable].join(', ')}): the cascade only resolves a display config's own top-level slots, so these would serialize as the bare inherit sentinel. Declare them on the display's own schema instead.`);
-    }
-}